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search for synonyms #35
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I would also find such a feature useful. |
I think Ontobee can already search for synonyms. From: nicolevasilevsky [mailto:notifications@github.com] Could we add the ability to search for synonyms when searching ontologies in Ontobee? — Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues |
A search for "vertebral body' does not return 'bony vertebral centrum' A search for 'von Ebner's gland' does not return 'gustatory gland' From: ontoden <notifications@github.commailto:notifications@github.com> I think Ontobee can already search for synonyms. From: nicolevasilevsky [mailto:notifications@github.com] Could we add the ability to search for synonyms when searching ontologies in Ontobee? — Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues — The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. |
But the term 'bony vertebral centrum' is not a synonym of 'vertebral body': 'vertebral body' is indeed a synonym of 'body of vertebra'. The 'body of vertebra' is the label of the term. 'vertebral body' is its synonym. When you search 'vertebral body', Ontobee will return the 'body of vertebra' to you. It indicates that Ontobee can search the synonym. Oliver From: cindyJax [notifications@github.com] A search for "vertebral body' does not return 'bony vertebral centrum' A search for 'von Ebner's gland' does not return 'gustatory gland' From: ontoden <notifications@github.commailto:notifications@github.com> I think Ontobee can already search for synonyms. From: nicolevasilevsky [mailto:notifications@github.com] Could we add the ability to search for synonyms when searching ontologies in Ontobee? — Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues — The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. — Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues |
Maybe ontobee doesn't use the oboInOwl vocab? |
It's possible. Let me check it out. From: Chris Mungall [notifications@github.com] Maybe ontobee doesn't use the oboInOwl vocab? — Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues |
Any progress? This should be trivial? |
The reason why Ontobee could not retrieve synonyms from MP and UBERON is because these two ontologies and several others used: Ontobee by default used IAO:“alternative term” as synonyms. After we found the issue, I asked Edison to fix it. Thanks, Edison, for working on this. This should be fixed in Ontobee by Edison for now. Please check out. It appears that there are three other types of “synonyms”: They appear not “exact”. We don’t know if we want to include these “synonyms” into our synonym searching function. I think we will need to obtain some consensus on this issue first before we implement it. Oliver From: nicolevasilevsky [mailto:notifications@github.com] Ontobee does not seem to retrieve synonyms from MP. Some examples: MP Term: increased desmoid tumor incidence MP term: abnormal cochlear hair cell development [image]https://cloud.githubusercontent.com/assets/6722114/6193697/b1c17b32-b372-11e4-8d20-6ef5e6867f89.png — Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues |
Hi Chris, From: He, Yongqun [mailto:yongqunh@med.umich.edu] It's possible. Let me check it out. From: Chris Mungall [notifications@github.com] Maybe ontobee doesn't use the oboInOwl vocab? Reply to this email directly or view it on GitHubhttps://github.com//issues/35#issuecomment-74348354. Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues |
Of course you will want to include the other synonym scopes |
I suggest that the broader and narrower synonym terms should be included in In the result section, those types of synonyms should be shown. Best, On Tue, Aug 4, 2015 at 4:21 PM, ontoden notifications@github.com wrote:
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The keyword searching function against has_exact_synonym, has_related_synonym, has_narrow_synonym and has_broad_synonym is now implemented in Ontobee. |
Great! Thanks, Edison! On Tue, Aug 4, 2015 at 4:48 PM, e4ong1031 notifications@github.com wrote:
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For example, has_exact_synonym: thorax blood vessel; blood vessel of thorax Now you can search these synonyms in Ontobee, for example, Oliver From: Asiyah Yu Lin [mailto:notifications@github.com] Great! Thanks, Edison! On Tue, Aug 4, 2015 at 4:48 PM, e4ong1031 <notifications@github.commailto:notifications@github.com> wrote:
— Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues |
Looks good to me. Thanks! On Tue, Aug 4, 2015 at 4:55 PM, ontoden notifications@github.com wrote:
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@e4ong1031 you rock! |
This has been a major issue for ontobee for a while, it's worth calling out this improvement, e.g. in a news page or tweet |
Good point. I have added this to the Ontobee news page: http://www.ontobee.org/news.php. Thanks. |
Could we add the ability to search for synonyms when searching ontologies in Ontobee?
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